LGBMDF: A cascade forest framework with LightGBM for predicting drug-target interactions

Prediction of drug-target interactions (DTIs) plays an important role in drug development. However, traditional laboratory methods to determine DTIs require a lot of time and capital costs. In recent years, many studies have shown that using machine learning methods to predict DTIs can speed up the drug development process and reduce capital costs. An excellent DTI prediction method should have both high prediction accuracy and low computational cost. In this study, we noticed that the previous research based on deep forests used XGBoost as the estimator in the cascade, we applied LightGBM instead of XGBoost to the cascade forest as the estimator, then the estimator group was determined experimentally as three LightGBMs and three ExtraTrees, this new model is called LGBMDF. We conducted 5-fold cross-validation on LGBMDF and other state-of-the-art methods using the same dataset, and compared their Sn, Sp, MCC, AUC and AUPR. Finally, we found that our method has better performance and faster calculation speed

The UDP-glucosyltransferase multigene family in Bombyx mori

<p>Abstract</p> <p>Background</p> <p>Glucosidation plays a major role in the inactivation and excretion of a great variety of both endogenous and exogenous compounds. A class of UDP-glycosyltransferases (UGTs) is involved in this process. Insect UGTs play important roles in several processes, including detoxication of substrates such as plant allelochemicals, cuticle formation, pigmentation, and olfaction. Identification and characterization of <it>Bombyx mori </it>UGT genes could provide valuable basic information for this important family and explain the detoxication mechanism and other processes in insects.</p> <p>Results</p> <p>Taking advantage of the newly assembled genome sequence, we performed a genome-wide analysis of the candidate UGT family in the silkworm, <it>B. mori</it>. Based on UGT signature and their similarity to UGT homologs from other organisms, we identified 42 putative silkworm UGT genes. Most of them are clustered on the silkworm chromosomes, with two major clusters on chromosomes 7 and 28, respectively. The phylogenetic analysis of these identified 42 UGT protein sequences revealed five major groups. A comparison of the silkworm UGTs with homologs from other sequenced insect genomes indicated that some UGTs are silkworm-specific genes. The expression patterns of these candidate genes were investigated with known expressed sequence tags (ESTs), microarray data, and RT-PCR method. In total, 36 genes were expressed in tissues examined and showed different patterns of expression profile, indicating that these UGT genes might have different functions.</p> <p>Conclusion</p> <p><it>B. mori </it>possesses a largest insect UGT gene family characterized to date, including 42 genes. Phylogenetic analysis, genomic organization and expression profiles provide an overview for the silkworm UGTs and facilitate their functional studies in future.</p

Experimental Long-Distance Decoy-State Quantum Key Distribution Based On Polarization Encoding

We demonstrate the decoy-state quantum key distribution (QKD) with one-way quantum communication in polarization space over 102km. Further, we simplify the experimental setup and use only one detector to implement the one-way decoy-state QKD over 75km, with the advantage to overcome the security loopholes due to the efficiency mismatch of detectors. Our experimental implementation can really offer the unconditionally secure final keys. We use 3 different intensities of 0, 0.2 and 0.6 for the pulses of source in our experiment. In order to eliminate the influences of polarization mode dispersion in the long-distance single-mode optical fiber, an automatic polarization compensation system is utilized to implement the active compensation.Comment: 4 pages,3 figure

Higher dietary diversity scores and protein-rich food consumption were associated with lower risk of all-cause mortality in the oldest old

Background & aims: Dietary diversity is widely advocated in national and international recommendations although whether the beneficial effects on survival or longevity still apply in the final phase of the lifespan remains understudied. We aimed to prospectively examine the association of dietary diversity, food items with all-cause mortality among the oldest old (80+) and determine whether dietary diversity recommendations were appropriate for this population. Methods: The study included 28,790 participants aged 80+ (9957 octogenarians, 9925 nonagenarians, and 8908 centenarians). A baseline dietary diversity score (DDS) was constructed based on nine food items of a food frequency questionnaire. Cox models with penalized splines evaluated non-linear associations of DDS as continuous variable with mortality to identify cut-offs of DDS. Results: We documented 23,503 deaths during 96,739 person-years of follow-up. Each one unit increase in DDS was associated with a 9% lower risk of mortality (adjusted hazard ratio (HR): 0.91; 95% confidential interval (CI): 0.90–0.92). Compared to participants whose DDS less than 2 scores, those with a DDS of 2, 3, 4, 5, and higher than 6 scores had a lower mortality risk, the HRs were 0.86 (0.82–0.89), 0.78 (0.75–0.81), 0.69 (0.66–0.72), 0.65 (0.62–0.68), and 0.56 (0.53–0.58) respectively, and a significant trend emerged (p \u3c 0.001). Protein-rich food items were associated with prominent beneficial effects on mortality including meat (HR and 95% CI for high vs low frequency: 0.70 (0.68–0.72)), fish and sea food (HR, 0.74 (0.72–0.77)), egg (HR, 0.75 (0.73–0.77)), and bean (HR, 0.80 (0.78–0.82)). Conclusions: Even after the age of 80, the DDS tool may offer a simple and straightforward mean of identifying and screening individuals at high risk for mortality. Recommendation of dietary diversity, especially consumption of protein-rich food, may be advocated to reduce mortality risk and promote longevity in the oldest old

The development and evaluation of individualized templates to assist transoral C2 articular mass or transpedicular screw placement in TARP-IV procedures: adult cadaver specimen study

OBJECTIVES: The transoral atlantoaxial reduction plate system treats irreducible atlantoaxial dislocation from transoral atlantoaxial reduction plate-I to transoral atlantoaxial reduction plate-III. However, this system has demonstrated problems associated with screw loosening, atlantoaxial fixation and concealed or manifest neurovascular injuries. This study sought to design a set of individualized templates to improve the accuracy of anterior C2 screw placement in the transoral atlantoaxial reduction plate-IV procedure. METHODS: A set of individualized templates was designed according to thin-slice computed tomography data obtained from 10 human cadavers. The templates contained cubic modules and drill guides to facilitate transoral atlantoaxial reduction plate positioning and anterior C2 screw placement. We performed 2 stages of cadaveric experiments with 2 cadavers in stage one and 8 in stage two. Finally, guided C2 screw placement was evaluated by reading postoperative computed tomography images and comparing the planned and inserted screw trajectories. RESULTS: There were two cortical breaching screws in stage one and three in stage two, but only the cortical breaching screws in stage one were ranked critical. In stage two, the planned entry points and the transverse angles of the anterior C2 screws could be simulated, whereas the declination angles could not be simulated due to intraoperative blockage of the drill bit and screwdriver by the upper teeth. CONCLUSIONS: It was feasible to use individualized templates to guide transoral C2 screw placement. Thus, these drill templates combined with transoral atlantoaxial reduction plate-IV, may improve the accuracy of transoral C2 screw placement and reduce related neurovascular complications

Analysis of risk factors affecting the postoperative drainage after a laparoscopic partial nephrectomy: a retrospective study

PurposeLaparoscopic partial nephrectomy (LPN) remains the most commonly used measure for treating localized renal cell cancer (RCC) with an increasing incidence of RCC ever since the 1990s. This study aimed to identify risk factors that affect the postoperative time of drainage and total drainage volume after LPN.MethodThe clinical data of 612 RCC patients who received LPN from January 2012 to December 2022 in our hospital, including the postoperative drainage time and total drainage volume, were retrospectively analyzed. Univariable and multivariable linear regression and correlation analyses were used to identify the correlations between 21 factors, which include gender, age, history of alcohol consumption, family history of RCC, body weight, body mass index (BMI), and operation time, postoperative drainage time, and total drainage volume.ResultsThe mean time of drainage was 3.52 ± 0.71 days (range: 2 to 8 days), with an average total drainage volume of 259.83 ± 72.64 mL (range: 50 to 620 mL). Both univariable and multivariable linear regression analyses revealed several statistically significant associations. Gender (p = 0.04), age (p = 0.008), smoking history (p &lt; 0.001), diabetes (p = 0.032), operation time (p = 0.014), and BMI (p = 0.023) were identified as significant factors associated with the time of drainage. On the other hand, age (p = 0.008), smoking history (p &lt; 0.001), diabetes (p = 0.006), and BMI (p = 0.016) emerged as independent risk factors influencing the total drainage volume.ConclusionThe duration of postoperative drainage was found to be associated with gender, age, smoking history, diabetes, operation time, and BMI. In contrast, the total drainage volume was primarily influenced by age, smoking history, diabetes, and high BMI following LPN. For patients with these conditions, meticulous attention to hemostasis and bleeding control is crucial during the perioperative period

Epidemiology of human anthrax in China, 1955-2014

Using national surveillance data for 120,111 human anthrax cases recorded during 1955-2014, we analyzed the temporal, seasonal, geographic, and demographic distribution of this disease in China. After 1978, incidence decreased until 2013, when it reached a low of 0.014 cases/100,000 population. The case-fatality rate, cumulatively 3.6% during the study period, has also decreased since 1990. Cases occurred throughout the year, peaking in August. Geographic distribution decreased overall from west to east, but the cumulative number of affected counties increased during 2005-2014. The disease has shifted from industrial to agricultural workers; 86.7% of cases occurred in farmers and herdsmen. Most (97.7%) reported cases were the cutaneous form. Although progress has been made in reducing incidence, this study highlights areas that need improvement. Adequate laboratory diagnosis is lacking; only 7.6% of cases received laboratory confirmation. Geographic expansion of the disease indicates that livestock control programs will be essential in eradicating anthrax